Sunday, December 12, 2010

Joseph Kulper: Brain viruses and strange equations to save the human race

Today I received a mysterious message:
My name is Joseph Kulper, I work as a geneticist at Celtran
Corporation, one of the world's leaders in bioengineering, and I'm
sending this message to you because I have discovered something very
important, something that has the potential to change everything we
know about human life. I'm not asking for anything from you, I don't
want you to reply or click anywhere, alI I'm asking of you is that you
watch the video I have posted on youtube. Search under my name 'joseph
kulper' and you will find it. It's for you that I'm posting this
video, for all of us, so please take just a moment to watch it.

It wasn't sent to me personally and has the appearance of hapless self-promotion or odd spam.

But I was curious, and I turned up "Kulper's" video, where he invites the viewer to "become part of something greater than yourself. You see the destructive effects of climate change are inevitable, and some sort of drastic action is required to save the human race. So what has Kulper done? Created the Elysium virus, designed to "speed up evolution" so that only the smartest will survive. Watch:


So what is this? This looks like a teaser promotional video, likely for Neill Blomkamp's new movie-in-progress, Elysium.

There are a bunch of images that flash for a fraction of a second during the video which presumably have clues in them. In particular, there are a series of equations at about 4:27. I don't recognize the equations, and they could just be a red herring. Take a look - any guesses?



I couldn't find out much about the movie itself, other than Sharlto Copley - who starred in Blomkamp's District 9 - is part of the cast, and that Matt Damon may join up as well.

Despite the buzz, there hasn't been much information regarding what the plot will actually be about. Another teaser video released in November shows mutant livestock:


So the movie involves global catastrophes and genetic engineering and a selective virus passed from mind to mind; it's apparently set in a dystopian near-future in which biotechnology has run amok.  So maybe it's an action-packed version of Oryx and Crake?

It could be interesting. I just hope there aren't any zombies.

Friday, December 10, 2010

Life Force

The few minutes I had to spend in the Institute’s waiting room were my least favorite part of coming up to visit my mother. It felt more like a dialysis room, the visitors sunk into the overly-soft couches and not speaking, just drinking orange juice and recovering. There were no magazines and no television, just cold air blowing from the vents and generic music flowing with it. I’d finished my juice and was beginning to brood on my dislike for overly air-conditioned buildings when my mother arrived attended by a nurse.


I kissed and hugged her, automatically asking how she was, mouthing the answer she always gave as she gave it again.


“I’m fine, same as always.”


It wasn’t strictly true, but true enough.

~ "Élan Vital" by K. Tempest Bradford

Last week Escape Pod republished K. Tempest Bradford's short story "Élan Vital".

The science part is handwavy, but I don't think that takes away from the story at all. The first time I read it, it was only a few months after my dad had passed away and it really hit home.

What would you be willing to give to keep someone you love alive?

Listen to and read "Élan Vital" at Escape Pod

Read "Élan Vital" by K. Tempest Bradford at Sybil's Garage


Image: "Free Souls Embrace" by D Sharon Pruitt on Flickr.  Shared under a Creative Commons Attribution 2.0 Generic license.

Tuesday, December 07, 2010

Mario Vargas Llosa: Fiction provides refuge and transforms the impossible into possibility

Peruvian writer andwinner of the 2010 Nobel Prize in Literature Mario Vargas Llosa,  gave a moving Nobel Prize lecture - "In Praise of Reading and Fiction" - about the importance of fiction to his life and to humanity.:
But thanks to literature, to the consciousness it shapes, the desires and longings it inspires, and our disenchantment with reality when we return from the journey to a beautiful fantasy, civilization is now less cruel than when storytellers began to humanize life with their fables. We would be worse than we are without the good books we have read, more conformist, not as restless, more submissive, and the critical spirit, the engine of progress, would not even exist. Like writing, reading is a protest against the insufficiencies of life. When we look in fiction for what is missing in life, we are saying, with no need to say it or even to know it, that life as it is does not satisfy our thirst for the absolute – the foundation of the human condition – and should be better. We invent fictions in order to live somehow the many lives we would like to lead when we barely have one at our disposal. 
And, when at age 11 there was a great upheaval in his family life, Vargas Llosa found reading and writing to be a great comfort:

I lost my innocence and discovered loneliness, authority, adult life, and fear. My salvation was reading, reading good books, taking refuge in those worlds where life was glorious, intense, one adventure after another, where I could feel free and be happy again. And it was writing, in secret, like someone giving himself up to an unspeakable vice, a forbidden passion. Literature stopped being a game. It became a way of resisting adversity, protesting, rebelling, escaping the intolerable, my reason for living. From then until now, in every circumstance when I have felt disheartened or beaten down, on the edge of despair, giving myself body and soul to my work as a storyteller has been the light at the end of the tunnel, the plank that carries the shipwrecked man to shore. 

And reading fiction transforms us, the readers:
From the cave to the skyscraper, from the club to weapons of mass destruction, from the tautological life of the tribe to the era of globalization, the fictions of literature have multiplied human experiences, preventing us from succumbing to lethargy, self-absorption, resignation. Nothing has sown so much disquiet, so disturbed our imagination and our desires as the life of lies we add, thanks to literature, to the one we have, so we can be protagonists in the great adventures, the great passions real life will never give us. The lies of literature become truths through us, the readers transformed, infected with longings and, through the fault of fiction, permanently questioning a mediocre reality. Sorcery, when literature offers us the hope of having what we do not have, being what we are not, acceding to that impossible existence where like pagan gods we feel mortal and eternal at the same time, that introduces into our spirits non-conformity and rebellion, which are behind all the heroic deeds that have contributed to the reduction of violence in human relationships. Reducing violence, not ending it. Because ours will always be, fortunately, an unfinished story. That is why we have to continue dreaming, reading, and writing, the most effective way we have found to alleviate our mortal condition, to defeat the corrosion of time, and to transform the impossible into possibility.
He's not talking about speculative fiction specifically, but I think it applies. To me science fiction is indeed a way of dreaming the impossible and getting lost in adventure and fantastic worlds.

In Vargas Llosa's Letters to a Young Novelist, he does write about the "fantastic" and "levels of reality" in fiction. But he also points out that any fiction is a rejection of reality:
Why would anyone who is deeply satisfied with reality, with real life as it is lived, dedicate himself to something as insubstantial and fanciful as the creation of fictional realities? Naturally, those who rebel against lie as it is, using their ability to invent different lives and different people, may do so for any number of reasons, honorable or dishonorable, generous or selfish, complex or banal. The nature of this basic questioning of reality, which to my mind lies at the heart of every literary calling, doesn't matter at all. What matters is that the rejection be strong enough to fuel the enthusiasm for a task as quixotic as tilting at windmills – the slight-of-hand replacement of the concrete, objective world of life as it is lived with the subtle and ephemeral world of fiction.
And that rejection of reality can have real world consequences.
When readers are faced with the real world, the unease fomented by good literature may, in certain circumstances, even translate itself into an act of rebellion against authority, the establishment, or sanctioned beliefs. 
That's why the Spanish Inquisition distrusted works of fiction and subjected them to strict censorship [... ] [Using the pretext that] these wild tales might distract the Indians from the worship of God, the only serious concern of a theocratic society.

While you might argue that science fiction doesn't qualify as "good literature", I think that SF doesn't only show a reader the possibility of adventure and a depiction of the world-as-it-might-be. It also can provide a framework that allows seeing the world through the lens of science and technology.  It gives us a glimpse at a way to "... alleviate our mortal condition, to defeat the corrosion of time, and to transform the impossible into possibility" using knowledge and engineering, rather than through supernatural forces. And that is a powerful notion.

Read the entire speech: "In Praise of Reading and Fiction"

Letters to a Young Novelist at Amazon.com

Also check out Daniel Salvo's article about SF in Peru for the World SF News Blog.

Friday, December 03, 2010

Medical aid on distant worlds


The colony sat at the edge of a river, under an evening sky of breathable air set with three brilliant, fast-moving moons. Beds of glorious flowers dotted the settlement, somewhere in size between a large town and a small city. The buildings of foamcast embedded with glittering native stone were graceful, well-proportioned rooms set around open atria. Minimal furniture, as graceful as the buildings; even the machines blended unobtrusively into the lovely landscape. The colonists had taste and restraint and a sense of beauty. They were all dead.

~ "Ej-Es" by Nancy Kress
The November issue of Lightspeed Magazine republishes Nancy Kress's 2003 short story "Ej-Es". The tale follows a member of a team of "medicians" that lands on a colony planet where the inhabitants have been wiped out by an unknown disease.

In an interview with Lightspeed, Kress explains the inspiration for the medical team:
The Corps is based on USAMRIID, the United States Army Medical Research Institute for Infectious Diseases. This group has joined (and sometimes waged turf wars with) the CDC in fighting epidemics in third-world countries; they also have shared jurisdiction, with FEMA and the CDC, for any bioterrorist attacks here (potential turf wars).
Of course USAMRIID's web site makes it sound like they are quite chummy with the CDC. It's true, though, that the vaccines, antivirals and antitoxins developed by USAMRIID have been used to help people around the world.

I like the idea that when humanity does spread through space, there will be a medical organization equipped to help identify and fight the unexpected diseases we are likely to encounter.  I think it unlikely that viruses or microbes evolved on alien worlds to infect the local life forms would find humans to be good hosts, but who knows? That's why we'd need medical experts ready for the unexpected.

The other scientific aspect of "Ej-Es" is that the infections seem to have induced conversations with invisible companions.  In an accompanying article, neuroscientist The Evil Monkey takes a look at the science of how a brain malfunctions and seizures could lead to visions. He writes:
How is it possible for a sane, sober, rational human to see things that aren’t there, and that maybe don’t even exist? Because your mind is your reality, that’s how. And your mind only exists because your brain exists. And your reality only reflects REALITYTM inasmuch as the information your brain processes accurately represents the world. Which, of course, then begs the question: what happens to us sane, sober, rational humans when our brains misfire?
Read the article to learn how our brain affects our perception of the outside world.

Read "Ej-Es" by Nancy Kress

How far was that?

Science comedian Brian Malow at 2010 WonderFest riffing on bad science in Star Wars the movie and Star Wars the novel.

Yes, it's an easy target. No, it has nothing to do with biology. But hey, it's Friday night!

See the full-size video at ForaTV

Thursday, December 02, 2010

One creature's poison is another one's meat

Today NASA held a press conference announcing the first demonstration that organisms could use arsenic in place of phosphorus in their cells. Not surprisingly, science fiction got there first . . .

Kirk told [Bones] about the tabekh sauce. Bones nodded at that and said, "Yes, I've heard of it. I don't think you'd want to try it, though."
"Why not?"
"One of the other ingredients is arsenic."
Kirk blinked.
"Apparently they like the bitter taste," Bones said. "Also, the arsenides are pretty important in their diet. Klingons can get into horrible arsenide deficiencies if they're not careful, especially in stressful situations –"
~ Doctor's Orders by Diane Duane (1990)

While Klingons need a bit of arsenic in their diet, the element is a deadly poison to humans and most other Earthly life forms. A big part of what makes arsenic toxic is that it has very similar - but not identical - chemical properties as phosphorus, one of the fundamental building blocks of life.

Phosphorus is a component of the phospholipid molecules that form cellular membranes, the backbone of DNA and, importantly adenosine triphosphate (ATP).  ATP is a molecule our cells use to store and transport energy. When arsenic is present in cells it interferes with the formation of ATP, which eventually leads to cell death.   For for a visual demonstration of how arsenic can substitute for phosphorus in biomolecules, see the video at the bottom of this page

GFAJ-1 bacteria grown on arsenic.
 Because  of the similarities between the properties of arsenic and phosphorus it's natural to speculate that organisms could evolve so that they could use arsenic in place of phosphorus.  Dr. Felisa Wolfe-Simon, a geobiologist with the US Geological Survey had been testing that idea by studying bacteria living  in California's Mono Lake, which has naturally high arsenic levels.

Wolfe-Simon's work is funded by the NASA Astrobiology Institute, and back in March she explained why finding arsenic-based life would be an important step in possibly understanding alien life.
Dr Wolfe-Simon has theorised that there may be life that chose an “evolutionary pathway” to utilise arsenic. If such microbes existed, it could suggest that life started on our planet not once but at least twice. In turn this would help to support the idea that life is much more likely to have started elsewhere in the galaxy.
It's a pretty interesting speculation about alternative biochemistry,  and I don't think it's too surprising to find the idea has already been played with in science fiction. 

The best example I can think of is science fiction author and microbiologist Joan Slonczewski's novel Brain Plague (Amazon.com). The story is about sentient arsenic-dependent microorganisms called "micros" that live in colonies in human hosts.
"Oh Great One" the letters flashed green. "Our growing children need arsenic."
"Arsenic" Chrys looked up. "Isn't that what the slaves kill for?" On the street they called it "ace."
Doctor Sartorius extended an appendage. A claw snapped open, revealing a white pill. "Micros evolved on a plenet full of arsenic. They need it as an essential mineral."
"But ace is poison"

"It's a controlled substance," the doctor admitted. "But our dietary supplement traps the arsenic in special cagelike molecules that keep it out of your own cells. Only the micros can extract it."

~ Brain Plague by Joan Slonczewski (2000)
Slonczewski acknowledges fellow microbiologist Barry Rosen, who studies arsenic resistance in microbes, for "telling her about arsenic."

But until today, the idea was still speculation.  NASA held a press conference today to announce - after much wild speculation and hoopla - Wolfe-Simon's experiments had shown that the bacteria from Mono Lake could indeed use arsenic in place of phosphorus.

Wolfe-Simon and her team of researchers took samples of lake sediment containing bacteria (named GFAJ-1). The bacteria were placed in a medium in which all phosphorus has been removed, but arsenic was present - and they grew.  If arsenic was also removed from the medium, the bacteria stopped growing, so either phosphorus or arsenic are necessary. Their experiments further show that when phosphorus is not present, arsenic is incorporated into DNA, cellular membranes, proteins and other molecules where phosphorus is normally found.

It is important to note that the bacteria grow much better when phosphorus is present, which means that they aren't truly "arsenic based life". But the fact that the bacteria don't need phosphorus is a major finding that challenges the common wisdom as to what constitutes the necessary components for life. While carbon, oxygen, sulfur and nitrogen are still commonly required by all the living organisms that have been studied, now we know that an environment - on Earth or any other planet - without phosphorus may indeed support life if there is arsenic to take its place.

As Wolfe-Simon puts it:
"If something here on Earth can do something so unexpected, what else can life do that we haven't seen yet?"
Indeed!

For more about the science, check out posts by Athena Andreadis, Ed Yong, Sarah Goslee, PZ Myers, and Jef Akst.



Here is an overview of the study from Science magazine:




Edited to add: Carl Zimmer has an article in Slate about the technical criticisms that have appeared regarding the science in this paper: "Scientists see fatal flaws in the NASA study of arsenic-based life."

In particular, he points to University of British Columbia microbiologist Rosie Redfield's  scathing review of the article.  
Also see the responses by George Cody and Alex Bradley.

Technical Background:

Research of Felisa Wolfe-Simon

Wolfe-Simon F, et al. "Did nature also choose arsenic?" International Journal of Astrobiology 8(2):69-74 (2009) (pdf)

Wolfe-Simon F., et al "A Bacterium That Can Grow by Using Arsenic Instead of Phosphorus" Science Express (2010) DOI: 10.1126/science.1197258 (abstract only without subscription).

NASA scientists have discovered a new extreme-loving microorganism in California's exotic Mono Lake  (2003) - note that this is a different organism, Spirochaeta americana. Mono Lake is full of weirdness!